Analysis of the algorithm: From embeddings to prioritized genes.

The algorithm transformed the similarity matrix to make it compatible with the embedding process. Once this was done for each network and embedding type, it was integrated by embedding type. Below there is a general analysis of the properties of each matrix in the different phases of the process, including the graph building process for each layer.

Annotations Properties

Table 1. Annotation descriptors.

Net Min Max Average Standard_Deviation
biological_process 1 1051 8.271854223097758 20.64383972786539
cellular_component 1 5160 7.257281553398058 82.4848318241769
disease 1 81 1.781670376463757 2.351512037356221
gene_PS 1 108 2.1512085441259132 5.036478784891552
gene_TF 1 5458 3.1027340513670256 71.99255468142772
gene_hgncGroup 1 844 2.4510855683269477 12.50842763548466
hippie_ppi 1 2956 89.24113906552391 152.25453953890658
molecular_function 1 6769 4.878140408546607 54.06507986648866
pathway 1 478 6.641383589266326 15.895125496783933
phenotype 1 1301 24.098699718652576 48.65371603412889
string_ppi 1 7324 612.3309525107683 499.667472060699

Individual Processing Graph steps

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Embedding Process

Table 2. Uncombined Embedding Matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
biological_process ct 16762x16762 280964644 280964644 1.0
biological_process el 16762x16762 280964644 280964644 1.0
biological_process ka 16762x16762 280964644 251263642 0.8942891832326063
biological_process node2vec 16762x16762 280964644 280964644 1.0
biological_process rf 16762x16762 280964644 280964644 1.0
cellular_component ct 17711x17711 313679521 313679521 1.0
cellular_component el 17711x17711 313679521 313679521 1.0
cellular_component ka 17711x17711 313679521 313679521 1.0
cellular_component node2vec 17711x17711 313679521 313679521 1.0
cellular_component rf 17711x17711 313679521 313679521 1.0
disease ct 4122x4122 16990884 16990884 1.0
disease el 4122x4122 16990884 16990884 1.0
disease ka 4122x4122 16990884 16909404 0.9952044873003665
disease node2vec 4122x4122 16990884 16990884 1.0
disease rf 4122x4122 16990884 16990884 1.0
gene_PS ct 3010x3010 9060100 8867656 0.9787591748435448
gene_PS el 3010x3010 9060100 5799252 0.640086974757453
gene_PS ka 3010x3010 9060100 98108 0.010828578051014889
gene_PS node2vec 3010x3010 9060100 9060100 1.0
gene_PS rf 3010x3010 9060100 5799252 0.640086974757453
gene_TF ct 3785x3785 14326225 14326221 0.9999997207917648
gene_TF el 3785x3785 14326225 14311093 0.9989437552460609
gene_TF ka 3785x3785 14326225 4984687 0.3479414151320393
gene_TF node2vec 3785x3785 14326225 14326225 1.0
gene_TF rf 3785x3785 14326225 14311093 0.9989437552460609
gene_hgncGroup ct 14252x14252 203119504 202830526 0.9985773005826166
gene_hgncGroup el 14252x14252 203119504 127988340 0.6301134922030924
gene_hgncGroup ka 14252x14252 203119504 2454766 0.012085328841685238
gene_hgncGroup node2vec 14252x14252 203119504 203119504 1.0
gene_hgncGroup rf 14252x14252 203119504 127988340 0.6301134922030924
hippie_ppi ct 15531x15531 241211961 241211961 1.0
hippie_ppi el 15531x15531 241211961 238609957 0.9892127903226159
hippie_ppi ka 15531x15531 241211961 418691 0.0017357804242551637
hippie_ppi node2vec 15531x15531 241211961 241211961 1.0
hippie_ppi rf 15531x15531 241211961 238609957 0.9892127903226159
molecular_function ct 17225x17225 296700625 296700625 1.0
molecular_function el 17225x17225 296700625 296700625 1.0
molecular_function ka 17225x17225 296700625 296700625 1.0
molecular_function node2vec 17225x17225 296700625 296700625 1.0
molecular_function rf 17225x17225 296700625 296700625 1.0
pathway ct 5526x5526 30536676 30536356 0.999989520797876
pathway el 5526x5526 30536676 24944472 0.8168692623912308
pathway ka 5526x5526 30536676 345452 0.011312691662969472
pathway node2vec 5526x5526 30536676 30536676 1.0
pathway rf 5526x5526 30536676 24944472 0.8168692623912308
phenotype ct 4860x4860 23619600 23619600 1.0
phenotype el 4860x4860 23619600 23619600 1.0
phenotype ka 4860x4860 23619600 23619600 1.0
phenotype node2vec 4860x4860 23619600 23619600 1.0
phenotype rf 4860x4860 23619600 23619600 1.0
string_ppi ct 18341x18341 336392281 336392281 1.0
string_ppi el 18341x18341 336392281 336392281 1.0
string_ppi ka 18341x18341 336392281 11249053 0.03344028277509733
string_ppi node2vec 18341x18341 336392281 336392279 0.9999999940545604
string_ppi rf 18341x18341 336392281 336392281 1.0

Table 3. Integrated Embedding Matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
integration_mean_by_presence ct 19195x19195 368448025 366892977 0.9957794644169962
integration_mean_by_presence el 19195x19195 368448025 366014501 0.9933952041132531
integration_mean_by_presence ka 19195x19195 368448025 340033915 0.9228816330335873
integration_mean_by_presence node2vec 19195x19195 368448025 366893807 0.9957817171092178
integration_mean_by_presence rf 19195x19195 368448025 366014501 0.9933952041132531
mean ct 19195x19195 368448025 366892977 0.9957794644169962
mean el 19195x19195 368448025 366014501 0.9933952041132531
mean ka 19195x19195 368448025 340033915 0.9228816330335873
mean node2vec 19195x19195 368448025 366893807 0.9957817171092178
mean rf 19195x19195 368448025 366014501 0.9933952041132531

Weight values